Organized thin films of novel poly(aryl ether ketone) derivative (PAEKd) were fabricated on monocrystalline silicon substrate by the method of spin casting. The PAEKd takes on two kinds of liquid crystalline states, nematic and smectic mesophases, at different temperatures. At this point, three types of PAEKd/Si heterostructures with different polymer phases, and hence the aligning orders of the molecular units, were prepared by carefully controlling the processing temperature. When comparing with silicon reference, all of the three heterostructures show a considerable decrease in the surface photovoltaic spectroscopy (SPS) response. A decreasing extent of them were found to have a close correlation with the degree of order of the molecules (DOM), i.e. crystalline-PAEKd-involved heterostructure shows the lowest surface photovoltaic intensity whereas that of nematic-PAEKd is the highest. These new photovoltaic behaviors were interpreted satisfactorily by considering the effect of DOM on blocking the transport of photogenerated carriers.